[BioC] new lumi and miRNA array data
cei at sanger.ac.uk
Mon May 5 20:51:43 CEST 2008
Hello Pan, et. al
I'm having some problems with a script that used to work before I upgraded
to BioCondcutr 2.2 (and thus lumi 1.6.0).
Sorry I don't have an example for this, but maybe you can point me out in
the right direction...
I get stuck when trying to run lumiT, this is what it looks like:
> raw <- lumiR(proFile, convertNuID=FALSE, inputAnnotation=FALSE)
Summary of BeadStudio output:
Illumina Inc. BeadStudio version 3.2.6
Normalization = none
Array Content = mouseMI_V1_R0.bgx.xml
Error Model = none
DateTime = 03/03/2008 16:39
Local Settings = en-GB
Major Operation History:
1 2008-05-05 19:41:48 2008-05-05 19:41:53
2 2008-05-05 19:41:53 2008-05-05 19:41:53
1 lumiR("Data/Sample_Gene_Profile.txt", inputAnnotation = FALSE)
2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh)
LumiBatch (storageMode: lockedEnvironment)
assayData: 386 features, 68 samples
element names: beadNum, detection, exprs, se.exprs
sampleNames: Brain 1 wt_(well=A1_MAFID=1), Brain 2 wt_(well=B1_MAFID=2),
Testes 3 KO_(well=H6_MAFID=48) (68 total)
varLabels and varMetadata description:
sampleID: The unique Illumina microarray Id
featureNames: mmu-let-7a, mmu-let-7b, ..., spike2-5240 (386 total)
fvarLabels and fvarMetadata description:
TargetID: The Illumina microarray identifier
experimentData: use 'experimentData(object)'
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
> lumiVst <- lumiT(raw, method="vst")
2008-05-05 19:36:37 , processing array 1
2008-05-05 19:36:37 , processing array 2
2008-05-05 19:36:39 , processing array 67
2008-05-05 19:36:39 , processing array 68
There were 50 or more warnings (use warnings() to see the first 50)
1: In lumiT(raw, method = "vst") ... :
Too few probes are detectable based on detection p-values!
Iteration method will be used for VST.
2: In log(u.bak) ... : NaNs produced
So, with lumi_1.4.0 I didn't get all these NaNs, now I do. Is this a
feature? Any suggestions on how to deal with micro-RNA array data with the
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